Variant report

Variant	rs6747563
Chromosome Location	chr2:95683120-95683121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95677663..95680622-chr2:95680904..95683785,2	K562	blood:
2	chr2:95681638..95683258-chr2:95684704..95687340,2	MCF-7	breast:
3	chr2:95682327..95685125-chr2:95786799..95789008,2	MCF-7	breast:
4	chr2:95668041..95669967-chr2:95681100..95683792,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144029	Chromatin interaction
ENSG00000242822	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11164117	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17802697	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4443026	0.85[CEU][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs67014278	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6709052	0.88[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs6721123	0.89[CEU][hapmap];0.81[CHB][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6723444	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587312	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6747563	CYP4F32P	cis	Esophagus Mucosa	GTEx
rs6747563	ZNF514	cis	Temporal Cortex	GTEx
rs6747563	ZNF514	cis	Whole Blood	GTEx
rs6747563	ZNF514	cis	Muscle Skeletal	GTEx
rs6747563	ZNF514	cis	Thyroid	GTEx
rs6747563	ZNF514	cis	parietal	SCAN
rs6747563	ACTR1B	cis	cerebellum	SCAN
rs6747563	ZNF514	cis	Artery Aorta	GTEx
rs6747563	ZNF514	Cis_1M	lymphoblastoid	RTeQTL
rs6747563	ZNF514	cis	cerebellum	SCAN
rs6747563	ZNF514	cis	Artery Tibial	GTEx
rs6747563	NMNAT2	trans	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95664400-95690600	Weak transcription	Right Atrium	heart
2	chr2:95664800-95686200	Enhancers	Fetal Thymus	thymus
3	chr2:95671000-95683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:95674400-95686000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:95676200-95685600	Weak transcription	Fetal Kidney	kidney
6	chr2:95678200-95683800	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:95678600-95683400	Enhancers	Brain Anterior Caudate	brain
8	chr2:95680600-95683600	Enhancers	Brain Hippocampus Middle	brain
9	chr2:95680600-95683600	Enhancers	Fetal Muscle Leg	muscle
10	chr2:95681200-95685000	Weak transcription	Fetal Lung	lung
11	chr2:95681600-95684800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:95681600-95688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:95682200-95683200	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:95682200-95685800	Enhancers	Esophagus	oesophagus
15	chr2:95682200-95690000	Enhancers	Brain Substantia Nigra	brain
16	chr2:95682400-95683800	Enhancers	Placenta	Placenta
17	chr2:95682400-95684000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr2:95682600-95683400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:95682600-95684000	Strong transcription	Thymus	Thymus
20	chr2:95682600-95685600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:95682800-95683200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:95682800-95683600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:95683000-95684000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:95683000-95684200	Weak transcription	Brain Angular Gyrus	brain

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